Extensive genome-wide duplications in the eastern oyster (Crassostrea virginica)

Abstract

Genomic structural variation is an important source of genetic and phenotypic diversity, playing a critical role in evolution. The recent availability of a high-quality reference genome for the eastern oyster, Crassostrea virginica , and whole-genome sequence data of samples from across the species range in the USA, provides an opportunity to explore structural variation across the genome of this species. Our analysis shows significantly greater individual-level duplications of regions across the genome than that of most model vertebrate species. Duplications are widespread across all ten chromosomes with variation in frequency per chromosome. The eastern oyster shows a large interindividual variation in duplications as well as particular chromosomal regions with a higher density of duplications. A high percentage of duplications seen in C. virginica lie completely within genes and exons, suggesting the potential for impacts on gene function. These results support the hypothesis that structural changes may play a significant role in standing genetic variation in C. virginica , and potentially have a role in their adaptive and evolutionary success. Altogether, these results suggest that copy number variation plays an important role in the genomic variation of C. virginica . This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

Dynamic evolutionary history of spiralian‐specific TALE homeobox genes in mollusks

“…Similarly, single SPILE‐E genes were found in gastropods, chitons, monoplacophorans, and most bivalves, but no SPILE‐E genes were found in cephalopods (Figure 2). SPILE‐D and ‐E gene duplications were found in the oyster Crassostrea virginica ; however, considering the high sequence similarity of the duplicated genes at the nucleotide level (99% identity) and recent reports on intraspecific chromosome duplication within this species (Modak et al, 2021), it is thought that these duplications occurred in recent years. Together, these results suggest that the ancestor of mollusks had a single SPILE‐D and ‐E gene and that gene duplications occur rarely in the mollusk lineage.…”

Pearls of wisdom—a Theo Murphy issue on molluscan genomics

“…Thus, work by Calcino et al [11] and others [12] using recently published complete genomes from representatives of eight wild-caught mollusc species to investigate the prevalence of hemizygous regions has implications for understanding genome dynamics across the other animal phyla. For similar benefit, Modak et al [13] assess copy number variation in oyster.…”

Diversification of the aquaporin family in geographical isolated oyster species promote the adaptability to dynamic environments

“…In this context, oysters represent an attractive model for studying the detailed mechanism in stress adaptation. Genetic and phenotypic diversity derived from genomic structural variation play a critical role in adaptation to the dynamic environments during the process of evolution [ 6 , 7 ]. Understanding the genome diversity of oysters at species level is central to revealing the adaptation mechanism to the varietal environments.…”

“…In order to understand the enhanced tolerance to the varietal environmental conditions in oysters, we have now conducted the duplication and deletion of the AQP family in Crassostrea based on the genome wide comparison. Three widely harvested oysters including the Crassostrea gigas (Cgi, Pacific oyster) that natively originated along the coasts of northeastern Asia [ 27 ], the Crassostrea hongkongensis (Chk, Hong Kong oyster) that cultivated surrounding the coastal of the Pearl River Delta in southern China [ 7 ] and the Crassostrea virginica (Cvi, Eastern oyster) that distribute from Gulf of Mexico to the Gulf of St. Lawrence along the Eastern Atlantic coast [ 28 ] were selected to perform this analysis. It is notable that the three selected oysters are distributed in different geographical environments and show long evolutionary distances [ 1 ].…”